Need help with water problem

This only happens when I build maps in TF2, it's never happened to me when I worked in HL2 or CS:S. Some basic information:

Sky: sky_day02_05Water: water/water_2fort

All water brushes have water on the top face, nodraw on the rest, and no attached entities.

The compile log is attached, and I took a pair of screenshots to illustrate what I'm talking about. I see right through the top surface of the water and I can see the skybox right through where the water surface should be! Beneath the water, everything is perfect. I've never really learned much about water because Ive never had a problem with it.

When building this map it was on normal, when built with fast on BSP/VIS/RAD all of the water surface looks completely flat and underwater looks like a above water scene.